Chromatin structure, compaction and remodeling at the micro and nanometer scale have fundamental roles in many biological events. Chromatin compaction produces heterogeneity of the cell nucleus which results in structural and transport properties which have been only partially studied. Although the nucleosome structure has been in part deciphered, the topology of chromatin structure at the micron scale remains unresolved. In this work, we studied chromatin organization using the orbital 3D tracking technique. This method provides insight of local structure and transport properties at the nano scale by following the trajectories of gold nanoparticle that are trapped in the chromatin. Using two-photon excitation, the fluorescence of fluorophores that are in the nanometer proximity to the gold particle is strongly enhanced. We have recently shown that metallic NPs do not bleach or blink upon continuous illumination, are extremely stable, very bright and their luminescence spans over the visible spectrum. These characteristics allow us to track them for minutes thus providing 3D trajectories appreciably longer than those based on fluorescent proteins or quantum dots. For this study we have analyzed the motion of a large number of nanoparticles incorporated inside the nucleus of NIH3T3 live cells. By tracking with high precision in 3D these nanoparticles we can have ~5 – 30 minutes long trajectory. In ~30% of the cases, we have observed that the NPs remain in regions of apparent confined motion (clusters) and eventually they undergo a long (in the micrometer range) excursion. We have found that the NPs within the clusters move faster than when travelling between clusters. These results suggest a topology for the chromatin made of cavities where the NP can move fast. These cavities are connected by channels where the particles move slowly but in a constant direction. Additionally, we express histones in NIH3T3 cells with different colors of fluorescent proteins. We show that as the NP moves along the trajectory, the emission changes alternatively between the two colors indicating that the NP is sensing the local chromatin environment.